Adding --copy-numbers to `guppy mft`.
Lengthening branches on the first pass through the tree.
Adding Nbc.
Refactoring to Tax_taxonomy.get_rank_index.
Adding bootstrapping to Nbc.
Adding an initial implementation of `guppy nbc`.
Adding Alignment.ungap.
Cleaning up/documenting/improving code.

This also allows `guppy nbc` to run on multiple processors, properly handles
gap vs. uninformative sites in sequences, and slightly decreases the number of
allocations done.
Adding a rectangular transpose to matrices.
Adding a more optimized matrix/vector multiplication.

This also updates Nbc to use said optimized multiplication and Multiprocessing
to not spawn processes if told to spawn 0 children.
comments for Aaron's code
Merge branch 'release' into 233-guppy-nbc
Tidying code; adding some BA[12].fill calls.
comments
Refactor to Nbc.Classifier.of_refpkg.
Allowing list flags to be Needs_argument.
Replaced the multiclass view with a table.

`guppy classify` will now also do NBC classification, as well as hybrid
pplacer/NBC classification. As a result, `guppy nbc` was removed.

`rppr prep_db` doesn't need flags or create a params table anymore, as `guppy
classify` is the only thing that needs the data what was previously being put
in the params table.

Tabular output was also removed from `guppy classify` as it doesn't seem useful
anymore.
Adding some remarks about new Guppy_classify functions.
decoupling boot_rows from n_boot
a rejecting version of NBC bootstrap